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Extending Gene Ontology in the Context of Extracellular RNA and Vesicle Communication

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Extending Gene Ontology in the Context of Extracellular RNA and Vesicle Communication UC San Diego UC San Diego Previously Published Works Title Extending gene ontology in the context of extracellular RNA and vesicle communication. Permalink https://escholarship.org/uc/item/7wt8r2d9 Journal Journal of biomedical semantics, 7(1) ISSN 2041-1480 Authors Cheung, Kei-Hoi Keerthikumar, Shivakumar Roncaglia, Paola et al. Publication Date 2016 DOI 10.1186/s13326-016-0061-5 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Cheung et al. Journal of Biomedical Semantics (2016) 7:19 DOI 10.1186/s13326-016-0061-5 RESEARCH Open Access Extending gene ontology in the context of extracellular RNA and vesicle communication Kei-Hoi Cheung1,2,21*, Shivakumar Keerthikumar3,21, Paola Roncaglia4,22, Sai Lakshmi Subramanian5,21, Matthew E. Roth5,21, Monisha Samuel3, Sushma Anand3, Lahiru Gangoda3, Stephen Gould6,21,23, Roger Alexander7,21, David Galas7,21, Mark B. Gerstein8,9,10,21, Andrew F. Hill3,24, Robert R. Kitchen8,21, Jan Lötvall11,24, Tushar Patel12,21, Dena C. Procaccini13,21, Peter Quesenberry14,21,24, Joel Rozowsky8,10,21, Robert L. Raffai15,21, Aleksandra Shypitsyna4,22, Andrew I. Su16,21, Clotilde Théry17,24, Kasey Vickers18,21, Marca H.M. Wauben19,24, Suresh Mathivanan3,21,24, Aleksandar Milosavljevic5,21 and Louise C. Laurent20,21* Abstract Background: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. Methods: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO. In addition, we have initiated an ongoing process of extractions of gene product annotations associated with these terms from Vesiclepedia and ExoCarta, conversion of the extracted annotations to Gene Association File (GAF) format for batch submission to GO, and curation of the submitted annotations by the GO Consortium. As a use case, we have incorporated some of the GO terms into annotations of samples from the exRNA Atlas and implemented a faceted search interface based on such annotations. Results: We have added 7 new terms and modified 9 existing terms (along with their synonyms and relationships) to GO. Additionally, 18,695 unique coding gene products (mRNAs and proteins) and 963 unique non-coding gene products (ncRNAs) which are associated with the terms: “extracellular vesicle”, “extracellular exosome”, “apoptotic body”,and “microvesicle” were extracted from ExoCarta and Vesiclepedia. These annotations are currently being processed for submission to GO. Conclusions: As an inter-community effort, we have made a substantial update to GO in the exRNA context. We have also demonstrated the utility of some of the new GO terms for sample annotation and metadata search. Keywords: Ontology, Extracellular RNA, Extracellular vesicle, Metadata, Faceted search, Atlas * Correspondence: [email protected]; `[email protected] 1Department of Emergency Medicine, Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA 20Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA Full list of author information is available at the end of the article © 2016 Cheung et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Cheung et al. Journal of Biomedical Semantics (2016) 7:19 Page 2 of 9 Background that uninfected chick and mammalian cells release RNA- Extracellular RNAs (exRNAs) are broadly defined as containing vesicles ([21]). However, these non-viral EVs RNAs that are present in the acellular portions of bio- remained largely uninvestigated for decades. EVs re- fluids, such as body fluids (blood, cerebrospinal fluid, entered the literature in the late 1960’swithdescriptions bile, lymph, vitreous humour, amniotic fluid, ascites, of calcifying matrix vesicles released by chondrocytes pleural, pericardial and peritoneal fluids, etc.), secretions ([22]) and vesicular ‘dust’ released by platelets ([23]). (saliva, urine, sweat, tears, milk, seminal fluid, etc.), and These and other such vesicles are now commonly referred cell and tissue culture supernatants. RNA sequencing to as ‘exosomes,’ a term coined by Trams et al. in 1981 analyses of exRNAs demonstrate that they represent al- ([24]) to refer to secreted vesicles that “may serve a most the entire range of cellular RNA species, including physiologic function”, including both small vesicles of rRNAs, tRNAs, mRNAs, miRNAs, piRNAs, lncRNAs, ~100 nm in diameter, and larger vesicles of ~600 nm and circular RNAs ([1–5]). However, the profiles of cel- diameter or greater. lular and exRNAs are not identical, as some cellular This first definition of the term ‘exosome’ has been RNAs appear to be highly enriched in the exRNA frac- subsequently overlooked at least twice, first in 1987 by tion, while others appear to be significantly underrepre- investigators studying the vesicular secretion of the sented, and still others lie between these extremes of transferrin receptor, who adopted a more restrictive def- enrichment or exclusion. inition of the term, conflating it with a delayed mode of Among the many reasons cells might release exRNAs, vesicle secretion in which the vesicles bud at endosome perhaps the most intriguing possibility is that exRNAs membranes to create a multivesicular body (MVB), might contribute to intercellular communication. Export followed later by MVB fusion with the plasma mem- of exRNAs may also be used to eliminate undesired brane to release the vesicles into the extracellular space RNAs from the originating cell. Finally, some exRNAs ([25]). In 1997, investigators studying an RNA-degrading might be generated in a nonspecific manner, either by protein complex adopted the term ‘exosome’, this time living cells (e.g. by a ‘bulk flow’ process) or as a conse- for an entirely unrelated intracellular biochemical entity quence of cell death (reviewed in [6]). ([26]). Not surprisingly, other investigators have come to ExRNAs appear to be universally associated with carrier different conclusions about which definition holds scien- vehicles, likely due to the rapid degradation of unpro- tific precedent, resulting in variable use of the term ‘exo- tected RNAs in biofluids ([4, 7–10]). The biochemical some’ in different laboratories. EV-related nomenclatures properties of these carriers are likely to be the primary de- are further complicated by the common use of additional terminant of the types and specific identities of exRNAs terms for secreted vesicles that are variably associated with that are secreted from cells, as well as their stability in the different biophysical properties or biogenesis pathways, as extracellular milieu. The first exRNA carriers identified wells as terms based on the cell type or tissue of origin. were RNA viruses, which carry not only viral RNAs, but The former include ‘ectosomes’ (which refer to EVs that also varying levels of host-encoded RNAs. For example, are produced by budding from the plasma membrane retroviruses typically carry two host tRNAs and sub- ([27, 28]) and ‘microvesicles’ (which are frequently oper- stoichiometric levels of host mRNAs from the cell in ationally defined as EVs that pellet at moderate centrifuga- addition to two copies of the viral RNA genome and key tion speeds (~10,000–20,000 xg) [29]), while the latter viral proteins ([11–16]). In fact, retrovirally infected cells include ‘prostasomes’ ([30]), ‘epididymosomes’ ([31]), produce more “empty” virus-like particles (VLPs) than in- ‘immunosomes’ ([32, 33]), ‘oncosomes’ ([34]), and ‘platelet fectious virions. These VLPs have failed to encapsulate the dust’ ([23]). There are even some vesicle names that refer viral RNA genome, but can carry as much as 10 kb of to observed biological activities (e.g. ‘tolerosomes’ ([35]) host-encoded RNA ([17]). More recently, it has been dis- and ‘calcifying matrix vesicles’ ([22]). covered that virally uninfected cells also release RNAs into The International Society for Extracellular Vesicles the extracellular space, and that these exRNAs are associ- (ISEV) has previously attempted to clarify the nomencla- ated with extracellular vesicles (EVs), lipoproteins (LPPs, ture in this field. Its primary achievements have been to most commonly HDLs ([10, 18]), LDLs ([18, 19])), and (1) introduce the term ‘extracellular vesicle (EV)’ as a ribonucleoprotein particles (RNPs, most commonly general term intended to encompass all secreted vesicles, Ago2-containing RNPs ([9, 20]). While the biogenic and encourage its broad acceptance, and (2) encourage
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